How do I get objects with visibility toggled off in a file saved in Blender 2.79 to be visible in Blender 2.8?
There are a few visibility options in Blender 2.80 that confuse new users (and also experienced ones). By default, you can only see the hide in viewport one, which is represented by the eye icon. However, there is also another option called disable in viewport. You have to enable a filter option first from the filter popup on the right to even see this icon (looks like a small TV screen):



Then you'll be able to see and toggle it from the Outliner:



Its purpose is to hide an object from a collection instance. So if you instance Collection from the example in the screenshots, the Plane object would be hidden. If you only used the eye icon, the instance will show the Plane object regardless.